Argonaute: the core of small RNA effector complex

2013 Fiscal Year Final Research Report

• Project Area: Functional machinery for non-coding RNAs
• Project/Area Number: 21115002
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: TOMARI Yukihide 東京大学, 分子細胞生物学研究所, 教授 (90447368)
• Co-Investigator(Kenkyū-buntansha): SIOMI Mikiko 東京大学, 大学院理学系研究科, 教授 (20322745)
• Project Period (FY): 2009-07-23 – 2014-03-31
• Keywords: 遺伝子 / 発現制御 / 核酸 / 蛋白質

Research Abstract

At the core of the small RNA effector complex lie Argonaute family proteins, which can be divided into ubiquitous AGO subfamily and gonad-specific PIWI subfamily. We have made a series of important discoveries about the effector complex assembly and target silencing functions of AGO-clade small RNAs, including our finding that the N domain of AGO plays a critical role in separating the two small RNA strands within AGO to mature the effector complex. We have also successfully reconstituted the core part of the piRNA biogenesis pathway in vitro, paving a new path to biochemical understanding of PIWI-clade small RNAs.

Research Products

• [Journal Article] Yb integrates piRNA intermediates and processing factors into perinuclear bodies to enhance piRISC assembly (2014)
  • Author(s): Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani, MK, Saito K, Okano H, Siomi H and Siomi MC
  • Journal Title: Cell Rep Volume: (in press)
  • Peer Reviewed
• [Journal Article] Molecular Insights into microRNA-Mediated Translational Repression in Plants (2013)
  • Author(s): Iwakawa HO, Tomari Y
  • Journal Title: Mol Cell Volume: 52(4) Pages: 591-601
  • Peer Reviewed
• [Journal Article] Poly(A)-Specific Ribonuclease Mediates 3'-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs (2013)
  • Author(s): Yoda M, Cifuentes D, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ, Tomari Y
  • Journal Title: Cell Rep Volume: 5(3) Pages: 715-726
  • Peer Reviewed
• [Journal Article] Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly (2013)
  • Author(s): Endo Y, Iwakawa HO, Tomari Y
  • Journal Title: EMBO Rep Volume: 14(7) Pages: 652-658
  • Peer Reviewed
• [Journal Article] Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins (2013)
  • Author(s): Izumi N, Kawaoka S, Yasuhara S, Suzuki Y, Sugano S, Katsuma S, Tomari Y
  • Journal Title: RNA Volume: 19(7) Pages: 896-901
  • Peer Reviewed
• [Journal Article] Piwi-interacting RNAs : biological functions and biogenesis (2013)
  • Author(s): Sato K, Siomi MC
  • Journal Title: Essays Biochem Volume: 54 Pages: 39-52
  • Peer Reviewed
• [Journal Article] The comprehensive epigenome map of piRNA clusters (2013)
  • Author(s): Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, Katsuma S
  • Journal Title: Nucleic Acids Res Volume: 41(3) Pages: 1581-1590
  • Peer Reviewed
• [Journal Article] Purification of dFMR1-Containing Complexes Using Tandem Affinity Purification (2013)
  • Author(s): Miyoshi K, Ogino A, Siomi MC, Siomi H
  • Journal Title: Trinucleotide Repeat Protocols (Methods in Molecular Biology) Volume: 1010 Pages: 111-121
  • Peer Reviewed
• [Journal Article] microRNAs mediate gene silencing via multiple different pathways in Drosophila (2012)
  • Author(s): Fukaya T, Tomari Y
  • Journal Title: Mol Cell Volume: 48(6) Pages: 825-836
  • Peer Reviewed
• [Journal Article] The N domain of Argonaute drives duplex unwinding during RISC assembly (2012)
  • Author(s): Kwak PB, Tomari Y.
  • Journal Title: Nat Struct Mol Biol Volume: 19(2) Pages: 145-151
  • Peer Reviewed
• [Journal Article] PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro (2011)
  • Author(s): Fukaya T, Tomari Y
  • Journal Title: EMBO J Volume: 30(24) Pages: 4998-5009
  • Peer Reviewed
• [Journal Article] The silkworm W chromosome is a source of female-enriched piRNAs (2011)
  • Author(s): Kawaoka S, Kadota K, Arai Y, Suzuki Y, Fujii T, Abe H, Yasukochi Y, Mita K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S
  • Journal Title: RNA Volume: 17(12) Pages: 2144-2151
  • Peer Reviewed
• [Journal Article] Recognition of the pre-miRNA structure by Drosophila Dicer-1 (2011)
  • Author(s): Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y
  • Journal Title: Nat Struct Mol Biol Volume: 18(10) Pages: 1153-1158
  • Peer Reviewed
• [Journal Article] 3' end formation of PIWI-interacting RNAs in vitro (2011)
  • Author(s): Kawaoka S, Izumi N, Katsuma S, Tomari Y
  • Journal Title: Mol Cell Volume: 43(6) Pages: 1015-1022
  • Peer Reviewed
• [Journal Article] Zygotic amplification of secondary piRNAs during silkworm embryogenesis (2011)
  • Author(s): Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S
  • Journal Title: RNA Volume: 17(7) Pages: 1401-1407
  • Peer Reviewed
• [Journal Article] Diazirine-containing RNA photocrosslinking probes for the study of siRNA-protein interactions (2010)
  • Author(s): Kuboe S, Yoda M, Ogata A, Kitade Y, Tomari Y, Ueno Y
  • Journal Title: Chem Commun Volume: 46(39) Pages: 7367-7369
  • Peer Reviewed
• [Journal Article] The microRNA pathway and cancer (2010)
  • Author(s): Kwak PB, Iwasaki S, Tomari Y
  • Journal Title: Cancer Sci Volume: 101(11) Pages: 2309-2315
  • Peer Reviewed
• [Journal Article] Making RISC (2010)
  • Author(s): Kawamata T, Tomari Y
  • Journal Title: Trends Biochem Sci Volume: 35(7) Pages: 368-376
  • Peer Reviewed
• [Journal Article] ATP-dependent human RISC assembly pathways (2010)
  • Author(s): Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S, Liu Q, Tomari Y
  • Journal Title: Nat Struct Mol Biol Volume: 17(1) Pages: 17-23
  • Peer Reviewed
• [Journal Article] Structural requirement of miRNAs for RISC-loading and slicer-independent unwinding (2009)
  • Author(s): Kawamata T, Seitz H, Tomari Y
  • Journal Title: Nat Struct Mol Biol Volume: 16(9) Pages: 953-960
  • Peer Reviewed
• [Journal Article] Argonaute-mediated translational repression (and activation) (2009)
  • Author(s): Iwasaki S, Tomari Y
  • Journal Title: Fly Volume: 3(3)
  • Peer Reviewed
• [Journal Article] The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes (2009)
  • Author(s): Kawaoka S, Hayashi N, Suzuki Y, Abe H, Sugano S, Tomari Y, Shimada T, Katsuma S
  • Journal Title: RNA Volume: 15(7) Pages: 1258-1264
  • Peer Reviewed
• [Journal Article] Drosophila Argonaute1 and Argonaute2 employ distinct mechanisms for translational repression (2009)
  • Author(s): Iwasaki S, Kawamata T, Tomari Y
  • Journal Title: Mol Cell Volume: 34(1) Pages: 58-67
  • Peer Reviewed
• [Presentation] Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex (2013)
  • Author(s): Tomari Y
  • Organizer: MBSJ2013
  • Place of Presentation: 神戸国際会議場,神戸
  • Year and Date: 20131203-06
• [Presentation] PIWI-interacting RNAs in transposon silencing in Drosophila (2013)
  • Author(s): Siomi MC
  • Organizer: MBSJ2013
  • Place of Presentation: 神戸国際会議場,神戸
  • Year and Date: 20131203-06
• [Presentation] Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex (2013)
  • Author(s): Tomari Y
  • Organizer: RiboClub 14^<th> Annual Meeting
  • Place of Presentation: Quebec, CANADA
  • Year and Date: 20130923-25
• [Presentation] 小さなRNAがはたらくしくみ (2013)
  • Author(s): 泊幸秀
  • Organizer: 生化学会若い研究者の会「第53回生命科学夏の学校」
  • Place of Presentation: 伊豆熱川,静岡県賀茂郡
  • Year and Date: 20130830-31
  • Invited
• [Presentation] カイコpiRNA生合性経路におけるBmQin の機能解析 (2013)
  • Author(s): 西田知訓,加藤弓子,岩崎由香,渋谷あおい,斎藤都暁,塩見春彦,塩見美喜子
  • Organizer: 第15回日本RNA 学会年会
  • Place of Presentation: 愛媛県民会館,松山
  • Year and Date: 20130723-25
• [Presentation] Assembly and function of RISC, IMBA (2013)
  • Author(s): Tomari Y
  • Organizer: 8^<th> Microsymposium on small RNAs
  • Place of Presentation: Vienna , AUSTRIA
  • Year and Date: 20130527-29
  • Invited
• [Presentation] Cell Biology of RNA Turnover (2013)
  • Author(s): Siomi MC
  • Organizer: EMBO Conference, Eukaryotic RNA Turn over from Structural Insights to Disease
  • Place of Presentation: Strasbourg, FRANCE
  • Year and Date: 20130421-24
  • Invited
• [Presentation] PIWI-interacting RNA Biogenesis in Drosophila (2013)
  • Author(s): Siomi MC
  • Organizer: Joint Conference of HGM 2013 and 21th International Congress of Genetics
  • Place of Presentation: Marina Bay Sands, SINGAPORE
  • Year and Date: 20130413-18
  • Invited
• [Presentation] Small RNAs (2013)
  • Author(s): Tomari Y
  • Organizer: 第7回日仏先端科学(JFFoS)シンポジウム
  • Place of Presentation: ロイヤルオークホテル,大津
  • Year and Date: 20130319-24
  • Invited
• [Presentation] 小さなRNA が働くしくみ (2013)
  • Author(s): 泊 幸秀
  • Organizer: 日本農芸化学会中央支部第169回例会 若手シンポジウム
  • Place of Presentation: 岐阜大学,岐阜
  • Year and Date: 2013-11-09
  • Invited
• [Presentation] Mechanisms of RNA silencing in animals and plants (2013)
  • Author(s): Tomari Y
  • Organizer: McGill University Biochemistry Department Seminar
  • Place of Presentation: Montreal, CANADA
  • Year and Date: 2013-09-26
  • Invited
• [Presentation] RNA サイレンシング複合体はどのように作られるのか? (2013)
  • Author(s): 泊 幸秀
  • Organizer: 理研セミナー
  • Place of Presentation: 理化学研究所,和光
  • Year and Date: 2013-08-29
  • Invited
• [Presentation] Biochemistry of small RNAS pathway in insects (2013)
  • Author(s): Tomari Y
  • Organizer: EMBL Grenoble Seminar
  • Place of Presentation: Grenoble,FRANCE
  • Year and Date: 2013-05-30
  • Invited
• [Presentation] Function and production of non-coding RNAs and their regulatory mechanisms (2012)
  • Author(s): Siomi MC
  • Organizer: MBSJ2012
  • Place of Presentation: 福岡国際会議場, 福岡
  • Year and Date: 20121211-14
• [Presentation] In vitro reconstitution of RISC assembly (2012)
  • Author(s): Tomari Y
  • Organizer: Cold Spring Harbor Conference Asia "RNA Biology"
  • Place of Presentation: Suzhou, CHINA
  • Year and Date: 20121008-12
  • Invited
• [Presentation] small RNA の生化学 (2012)
  • Author(s): 泊 幸秀
  • Organizer: 第14回日本RNA 学会年会
  • Place of Presentation: 東北大学,仙台
  • Year and Date: 20120718-20
• [Presentation] RNA サイレンシング複合体を組み立てるHsc70/Hsc90 シャペロン装置の役割 (2012)
  • Author(s): 泊 幸秀
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場, 名古屋
  • Year and Date: 20120620-22
• [Presentation] Biochemical Characterization of Dicer-independent miR-451 Biogenesis (2012)
  • Author(s): Yoda M, Tomari Y
  • Organizer: The 22^<nd> CDB Meeting" RNA Sciences in Cell and Developmental BiologyII "
  • Place of Presentation: 理研CDB, 神戸
  • Year and Date: 20120611-13
• [Presentation] microRNAs block translation initiation via GW182-dependent and -independent pathways (2012)
  • Author(s): Fukaya T, Tomari Y
  • Organizer: The 22^<nd> CDB Meeting" RNA Sciences in Cell and Developmental Biology II "
  • Place of Presentation: 理研CDB, 神戸
  • Year and Date: 20120611-13
• [Presentation] Assembly and function of RISC (2012)
  • Author(s): Tomari Y
  • Organizer: "Small Silencing RNA Biology and Mechanism": Fondation des Treilles
  • Place of Presentation: Turtour, FRANCE
  • Year and Date: 20120423-28
  • Invited
• [Presentation] PABP is not essential for microRNA-mediated translational repression and deadenylation (2012)
  • Author(s): Fukaya T, Tomari Y
  • Organizer: Keystone Symposia"Gene Silencing by small RNAS"
  • Place of Presentation: Vancouver, CANADA
  • Year and Date: 20120207-12
• [Presentation] Dicer is dispensable for asymmetric RISC loading in mammals (2012)
  • Author(s): Betancur JG, Tomari Y
  • Organizer: Keystone Symposia"Gene Silencing by small RNAS"
  • Place of Presentation: Vancouver, CANADA
  • Year and Date: 20120207-12
• [Presentation] Assembly and function of the RNAS-induced silencing complex (2012)
  • Author(s): Tomari Y
  • Organizer: Sydney RNA Workshop
  • Place of Presentation: Sydney, AUSTRALIA
  • Year and Date: 2012-11-27
  • Invited
• [Presentation] 小さなRNAがはたらくしくみ (2012)
  • Author(s): 泊 幸秀
  • Organizer: 情報機構「核酸医薬セミナー」
  • Place of Presentation: きゅりあん,東京
  • Year and Date: 2012-05-24
  • Invited
• [Presentation] Assembly and function of RISC (2012)
  • Author(s): Tomari Y
  • Organizer: the Institute of Human Genetics, Seminar
  • Place of Presentation: Montpellier, FRNACE
  • Year and Date: 2012-04-20
  • Invited
• [Presentation] Substrate recognition by Drosophila Dicer-1 (2011)
  • Author(s): Tsutsumi A, Kawamata T, Tomari Y
  • Organizer: Keystone Symposia, Mechanism and Biology of Silencing
  • Place of Presentation: Monterey, USA
  • Year and Date: 20110320-25
• [Presentation] In vivo recapitulation of primary piRNA biogenesis, Keystone Symposia (2011)
  • Author(s): Kawaoka S, Katsuma S, Tomari Y
  • Organizer: Mechanism and Biology of Silencing
  • Place of Presentation: Monterey, USA
  • Year and Date: 20110320-25
• [Presentation] How are piRNAs made? (2011)
  • Author(s): Tomari Y
  • Organizer: Keystone Symposia, Mechanism and Biology of Silencing
  • Place of Presentation: Monterey, USA
  • Year and Date: 20110320-25
  • Invited
• [Presentation] Assembly and function of RNA silencing complexs (2011)
  • Author(s): Tomari Y
  • Organizer: Special Seminar"Department of Biochemistry and Molecular Pharmacology"
  • Place of Presentation: University of Massachusetts Medical School, USA
  • Year and Date: 2011-10-13
• [Presentation] 内在性piRNA クラスタによる外来配列の認識 (2011)
  • Author(s): 小林真希,河岡慎平,光武宏,木内隆史,小林 淳,勝間 進,泊 幸秀
  • Organizer: RNA フロンティアミーティング2011
  • Place of Presentation: あいち健康プラザ,愛知県知多郡
  • Year and Date: 2011-08-31
• [Presentation] microRNAs : mechanism and function (2011)
  • Author(s): Tomari Y
  • Organizer: 16^<th> Anniversary Meeting of RNA Society
  • Place of Presentation: 京都国際会議場,京都
  • Year and Date: 2011-06-14
• [Presentation] Dictinct Roles of Argonaute N-terminal Region in RISC Assembly (2011)
  • Author(s): Pieter Bas Kwak, Yukihide Tomari
  • Organizer: 16^<th> Anniversary Meeting of RNA Society
  • Place of Presentation: 京都国際会議場,京都
  • Year and Date: 2011-06-14
• [Presentation] Poly(A)-binding protein id dispensable for miRNA-mediated deadenylation and translational repression (2011)
  • Author(s): Fukaya T, Tomari Y
  • Organizer: 16^<th> Anniversary Meeting of RNA Society
  • Place of Presentation: 京都国際会議場,京都
  • Year and Date: 2011-06-14
• [Presentation] 小さなRNA がはたらくしくみ (2011)
  • Author(s): 泊 幸秀
  • Organizer: 第13回フロンティア生命化学研究会シンポジウム
  • Place of Presentation: 東北大学、仙台
  • Year and Date: 2011-01-07
  • Invited
• [Presentation] Multilayer Checkpoints for miRNA Authenticity (2010)
  • Author(s): Tomari Y
  • Organizer: 19^<th> CDB Meeting"RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: 理研CDB,神戸
  • Year and Date: 20100510-12
  • Invited
• [Presentation] The Mirror-image Relationship between Unwinding and Target Recognition (2010)
  • Author(s): Yoda M, Tomari Y
  • Organizer: 19^<th> CDB Meeting"RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: 理研CDB,神戸
  • Year and Date: 20100510-12
• [Presentation] Substrate Recognition By Drosophila Dicer-1 (2010)
  • Author(s): Tsutsumi A, Tomari Y
  • Organizer: 19^<th< CDB Meeting"RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: 理研CDB, 神戸
  • Year and Date: 20100510-12
• [Presentation] Analysis of microRNA mediated deadnylationa in Drosphila (2010)
  • Author(s): 深谷雄志, 泊 幸秀
  • Organizer: BMB2010
  • Place of Presentation: 神戸国際会議場, 神戸
  • Year and Date: 2010-12-10
• [Presentation] ショウジョウバエ Dicer-1 による基質認識 (2010)
  • Author(s): 包 明久, 川俣 朋子, 泊 幸秀
  • Organizer: RNAフロンティアミーティング
  • Place of Presentation: 富士教育研究所、静岡県裾野
  • Year and Date: 2010-09-27
• [Presentation] ショウジョウバエDicer-1 による基質認識 (2010)
  • Author(s): 包 明久,川俣 朋子,泊 幸秀
  • Organizer: 第12回日本RNA学会年会
  • Place of Presentation: 一ツ橋記念講堂, 東京
  • Year and Date: 2010-07-27
• [Presentation] How to make RISC (2010)
  • Author(s): Tomari Y
  • Organizer: 5^<th> Microsymposium on Small RNAs
  • Place of Presentation: Vienna, AUSTRIA
  • Year and Date: 2010-05-17
  • Invited
• [Book] PIWI-interacting RNAs. Methods Mol Biol (2014)
  • Author(s): Siomi MC
  • Total Pages: XI, 249
• [Patent(Industrial Property Rights)] small RNA 二本鎖およびヘアピン型RNA の設計方法 (2009)
  • Inventor(s): 泊 幸秀, 川俣朋子, 依田真由子
  • Industrial Property Rights Holder: 東京大学
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2009-153798WO/2011/001965
  • Filing Date: 2009-06-29